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(Quote) Hi Sheila, Thanks for asking. I already figured it out, that is because all of ReadPosRankSum and MQRankSum values are 0.
(Quote) Thanks your so detailed reply. I am working on WES data of 1000+ subjects.The bellow is my thought : step 1: cut the chromosome several pieces based on same range (2,000,000bp), for example, the CHROM1 were cut to 13 pieces (2000000bp/piece,…
(Quote) Thank you @Geraldine_VdAuwera, I did do joint genotyping with GenotypeGVCFs. If GenotypeGVCFs defaulty convert the format from gvcf to vcf, I got the right vcf files now. The command is shown below: java -Xmx24G \ -jar $jar \ -V:VCF $list \…
(Quote) Hi Sheila, I modified my script according to the article you recommend. Since my data are WES data, I used the recommended "-an" arguments as shown below. -an QD -an FS -an SOR -an ReadPosRankSum -an MQRankSum -an InbreedingCo…
I figured it out by myself. 3Q. (Quote)
(Quote) There are many pathways directing to the gvcf files in "indi_1.list" It is easy to generate just use "ls" command.